Related papers: A statistical-mechanical study of evolution of rob…
We study the dynamics of phenotypically structured populations in environments with fluctuations. In particular, using novel arguments from the theories of Hamilton-Jacobi equations with constraints and homogenization, we obtain results…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
We study the low temperature dynamics of a two dimensional short-range spin system with uniform ferromagnetic interactions, which displays glassiness at low temperatures despite the absence of disorder or frustration. The model has a dual…
We propose a hybrid dynamical system approach to model the evolution of a pathogen that experiences different selective pressures according to a stochastic process. In every environment, the evolution of the pathogen is described by a…
Stochastic phenotype switching has been suggested to play a beneficial role in microbial populations by leading to the division of labour among cells, or ensuring that at least some of the population survives an unexpected change in…
The noise-induced pattern formation in a population dynamical model of three interacting species in the coexistence regime is investigated. A coupled map lattice of Lotka-Volterra equations in the presence of multiplicative noise is used to…
We argue that the stochastic dynamics of interacting agents which replicate, mutate and die constitutes a non-equilibrium physical process akin to aging in complex materials. Specifically, our study uses extensive computer simulations of…
Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
The role of the selection pressure and mutation amplitude on the behavior of a single-species population evolving on a two-dimensional lattice, in a periodically changing environment, is studied both analytically and numerically. The…
Jamming is a phenomenon shared by a wide variety of systems, such as granular materials, foams, and glasses in their high density regime. This has motivated the development of a theoretical framework capable of explaining many of their…
The exact quantum dynamics of the reduced density matrix of two coupled spin qubits in a quantum Heisenberg XY spin star environment in the thermodynamic limit at arbitrarily finite temperatures is obtained using a novel operator technique.…
We study the evolutionary dynamics of a phenotypically structured population in a changing environment , where the environmental conditions vary with a linear trend but in an oscillatory manner. Such phenomena can be described by parabolic…
We introduce and study a stochastic model for the dynamics of colonial species, which reproduce through fission or fragmentation. The fission rate depends on the relative sizes of colonies in the population, and the growth rate of colonies…
In statistical mechanics, the Potts model is a model for interacting spins with more than two discrete states. Neural networks which exhibit features of learning and associative memory can also be modeled by a system of Potts spins. A…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…
The protein folding problem has been fundamentally transformed by artificial intelligence, evolving from static structure prediction toward the modeling of dynamic conformational ensembles and complex biomolecular interactions. This review…
This study develops and analyzes a stochastic differential equation (SDE) model for the dynamics of hepatitis B virus (HBV) infection. While deterministic frameworks have yielded important insights into viral behavior, they cannot…
Understanding how stochastic and non-linear deterministic processes interact is a major challenge in population dynamics theory. After a short review, we introduce a stochastic individual-centered particle model to describe the evolution in…